I think the covariance matrix $\Sigma_{t-1}$ should be updated at each time $t$.
$$
\begin{equation}
p(x_t | u_t, x_{t-1}) \sim N(A_t x_{t-1}, A_t\Sigma_{t-1} A_t^T+R)
\end{equation}
$$
But your update is doing like below:
$$
\begin{equation}
p(x_t | u_t, x_{t-1}) \sim N(A_t x_{t-1}, A_t\Sigma_0 A_t^T+R)
\end{equation}
$$